Re: Question about openbabel ECFP fingerprint

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Re: Question about openbabel ECFP fingerprint

Geoffrey Hutchison-3
I am not sure if the current implementation of ECFP supports folding. It was contributed by Noel O'Boyle and NextMove - maybe they can comment.

-Geoff

On Oct 28, 2016, at 3:03 PM, Lirong Wang <[hidden email]> wrote:

Dear Dr. Hutchison,
  How are you? This is Lirong from school of pharmacy and I am an openbabel user. It is exciting the you have implemented the ECFP fingerprint in the latest version of openbabel. I am currently working on a project to index compounds in chembl database with ECFP(4 and 6).  I would like the ECFP fingerprint folded into either 1024 or 2048 bits to speed up the calculation. I used the commandline “babel -ismi test.smi -ofpt -xfECFP6 -xh test_ECFP6.fp”. But it seems not as the FP2 fingerprint(“babel -ismi test.smi -ofpt -xfFP2 -xh test_FP2.fp”). That is the fingerprints of the two compounds seem not the same length in test_ecfp6.fp. I also tried “–xN1024”, but still not the same length. Could you please help me on that? Thanks.
 
Best,
Lirong
 
 
*******************************
 
Lirong Wang, PhD
Assistant Professor
Computational Chemical Genomics Screening Center 
Department of Pharmaceutical Sciences/School of Pharmacy 
University of Pittsburgh
528 Salk Hall, 3501 Terrace Street
Pittsburgh, PA 15213
Phone:412-624-8118
 
<test_ECFP6.fp><test_FP2.fp>


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